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griffithlab / civic-meeting

Repo for advertising and organizing CIViC unconference/meeting activities
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Integrate CIViC with genome browsers (igv.js, JBrowse, ...) #33

Closed jrobinso closed 2 years ago

jrobinso commented 6 years ago

Integrate the CIViC DB with genome browsers including igv.js, JBrowse, and possibly IGV. This integration could take 2 forms, not mutually exclusive

(1) Link out to CIViC from VCF and other variant track types (e.g. SnpDB) and provide variant details in a popup.

(2) When zoomed in to “gene” level, query the CIViC API for variants as genes come into view and display as a track. Clicking on a variant would query the API and bring up details in a popup.

The motivation is to give researchers browsing their own variants in the genome browser easy access to CIViC data. igv.js does a similar thing now with Cravat.

If there is interest in this proposal I could outline an implementation approach here, or save it for the hackathon.

ahwagner commented 6 years ago

For progress on VCF exports, see in-progress issue: https://github.com/griffithlab/civicpy/issues/3

jrobinso commented 6 years ago

Thanks @ahwagner . BTW, I can't seem to apply a label (hackathon). Perhaps I don't have the right premissions?

ahwagner commented 6 years ago

No, it looks as though labels are one of those things that requires a team member to set (https://help.github.com/articles/repository-permission-levels-for-an-organization/). Thanks for the heads-up, adding the hackathon label now.

jrobinso commented 6 years ago

Powerpoint https://www.dropbox.com/s/kjl6l3a3i9yqw5t/Hackathon.pptx?dl=0 PDF https://www.dropbox.com/s/hzpqejij6kpuqhq/Hackathon.pdf?dl=0